Denes Turei
| Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: RELEASE_3_20 |
| git_last_commit: 3c7d7f1 |
| git_last_commit_date: 2024-10-29 10:41:00 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1456/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.14.0 (landing page) Denes Turei
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the OmnipathR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: OmnipathR |
| Version: 3.14.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OmnipathR_3.14.0.tar.gz |
| StartedAt: 2024-11-20 10:39:59 -0000 (Wed, 20 Nov 2024) |
| EndedAt: 2024-11-20 10:58:26 -0000 (Wed, 20 Nov 2024) |
| EllapsedTime: 1107.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: OmnipathR.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OmnipathR_3.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmnipathR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2024-11-20 10:40:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 10:40:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:40:54] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 10:40:54] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-11-20 10:40:54] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 10:40:54] [TRACE] [OmnipathR] Contains 1 files.
[2024-11-20 10:40:55] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-11-20 10:40:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 10:40:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:40:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 10:40:55] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2024-11-20 10:40:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-20 10:40:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:40:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-20 10:40:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:40:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-20 10:40:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:40:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-20 10:40:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:40:55] [TRACE] [OmnipathR] Cache locked: FALSE
It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2024-11-20 10:41:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 10:41:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:41:12] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 10:41:12] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-11-20 10:41:12] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 10:41:12] [TRACE] [OmnipathR] Contains 1 files.
[2024-11-20 10:41:12] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-11-20 10:41:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 10:41:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:41:12] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 10:41:12] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2024-11-20 10:41:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-20 10:41:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:41:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-20 10:41:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:41:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-20 10:41:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:41:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-20 10:41:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:41:12] [TRACE] [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotation_categories 103.965 0.052 105.571
curated_ligrec_stats 33.238 0.761 129.534
omnipath-interactions 29.387 1.069 74.238
filter_extra_attrs 25.706 0.176 27.998
nichenet_gr_network_omnipath 15.630 0.344 26.874
extra_attr_values 14.657 0.419 17.580
go_annot_download 13.863 0.511 27.881
extra_attrs_to_cols 12.950 0.108 13.092
giant_component 12.112 0.484 14.230
pivot_annotations 11.173 0.313 22.058
with_extra_attrs 10.994 0.127 12.633
nichenet_signaling_network_omnipath 10.493 0.071 14.170
omnipath_for_cosmos 10.246 0.191 63.700
extra_attrs 8.260 0.119 8.401
translate_ids_multi 8.236 0.028 17.533
has_extra_attrs 7.883 0.087 8.375
filter_by_resource 7.221 0.136 8.708
filter_intercell 6.877 0.202 10.634
static_table 6.677 0.147 11.387
find_all_paths 6.429 0.032 6.472
print_interactions 6.349 0.092 10.288
signed_ptms 5.569 0.004 6.620
curated_ligand_receptor_interactions 5.354 0.176 17.879
hpo_download 2.437 0.226 25.027
enzsub_graph 2.406 0.096 5.060
print_path_vs 2.295 0.024 5.623
translate_ids 1.347 0.004 20.189
ensembl_id_mapping_table 1.284 0.048 10.621
biomart_query 0.969 0.020 5.515
all_uniprots 0.878 0.055 26.050
uniprot_full_id_mapping_table 0.911 0.016 96.042
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package textcomp Error: Symbol \textrightarrow not provided by
(textcomp) font family ptm in TS1 encoding.
(textcomp) Default family used instead.
See the textcomp package documentation for explanation.
* checking PDF version of manual without index ... ERROR
* DONE
Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘OmnipathR’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2024-11-19 21:04:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-19 21:04:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 21:04:54] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-11-19 21:04:54] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-11-19 21:04:54] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-11-19 21:04:54] [TRACE] [OmnipathR] Contains 6 files. [2024-11-19 21:04:54] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-11-19 21:04:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-19 21:04:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 21:04:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-11-19 21:04:54] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2024-11-19 21:04:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-11-19 21:04:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 21:04:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-11-19 21:04:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 21:04:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-11-19 21:04:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 21:04:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-11-19 21:04:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 21:04:54] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-11-19 21:04:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-19 21:04:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 21:04:57] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-11-19 21:04:57] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-11-19 21:04:57] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-11-19 21:04:57] [TRACE] [OmnipathR] Contains 1 files. [2024-11-19 21:04:57] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-11-19 21:04:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-19 21:04:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 21:04:57] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-11-19 21:04:57] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2024-11-19 21:04:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-11-19 21:04:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 21:04:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-11-19 21:04:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 21:04:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-11-19 21:04:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 21:04:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-11-19 21:04:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 21:04:57] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #!/usr/bin/env Rscript
>
> #
> # This file is part of the `OmnipathR` R package
> #
> # Copyright
> # 2018-2024
> # Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> # File author(s): Alberto Valdeolivas
> # Dénes Türei (turei.denes@gmail.com)
> # Attila Gábor
> #
> # Distributed under the MIT (Expat) License.
> # See accompanying file `LICENSE` or find a copy at
> # https://directory.fsf.org/wiki/License:Expat
> #
> # Website: https://r.omnipathdb.org/
> # Git repo: https://github.com/saezlab/OmnipathR
> #
>
>
> library(testthat)
> library(OmnipathR)
[2024-11-20 10:57:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 10:57:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:57:19] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 10:57:19] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-11-20 10:57:19] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 10:57:19] [TRACE] [OmnipathR] Contains 21 files.
[2024-11-20 10:57:19] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-11-20 10:57:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 10:57:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:57:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 10:57:19] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2024-11-20 10:57:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-20 10:57:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:57:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-20 10:57:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:57:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-20 10:57:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:57:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-20 10:57:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:57:19] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
>
> proc.time()
user system elapsed
13.074 1.090 52.312
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.022 | 0.000 | 0.022 | |
| all_uniprots | 0.878 | 0.055 | 26.050 | |
| ancestors | 0.011 | 0.000 | 0.011 | |
| annotated_network | 0.811 | 0.071 | 4.330 | |
| annotation_categories | 103.965 | 0.052 | 105.571 | |
| annotation_resources | 0.084 | 0.004 | 0.980 | |
| annotations | 0.326 | 0.008 | 1.704 | |
| biomart_query | 0.969 | 0.020 | 5.515 | |
| bioplex1 | 0.012 | 0.000 | 0.012 | |
| bioplex2 | 0.012 | 0.000 | 0.012 | |
| bioplex3 | 0.057 | 0.000 | 0.057 | |
| bioplex_all | 0.012 | 0.000 | 0.012 | |
| bioplex_hct116_1 | 0.012 | 0.000 | 0.012 | |
| bma_motif_es | 0.363 | 0.047 | 1.857 | |
| bma_motif_vs | 0.215 | 0.011 | 1.123 | |
| chalmers_gem | 0.011 | 0.000 | 0.011 | |
| chalmers_gem_id_mapping_table | 0.010 | 0.000 | 0.011 | |
| chalmers_gem_id_type | 0.002 | 0.000 | 0.002 | |
| chalmers_gem_metabolites | 0.010 | 0.000 | 0.011 | |
| chalmers_gem_network | 0.011 | 0.000 | 0.011 | |
| chalmers_gem_raw | 0.011 | 0.000 | 0.011 | |
| chalmers_gem_reactions | 0.011 | 0.000 | 0.011 | |
| common_name | 0.035 | 0.003 | 0.038 | |
| complex_genes | 0.492 | 0.024 | 2.548 | |
| complex_resources | 0.115 | 0.004 | 1.008 | |
| complexes | 0.160 | 0.004 | 1.060 | |
| consensuspathdb_download | 0.001 | 0.000 | 0.001 | |
| consensuspathdb_raw_table | 0.011 | 0.000 | 0.011 | |
| cosmos_pkn | 0.000 | 0.000 | 0.001 | |
| curated_ligand_receptor_interactions | 5.354 | 0.176 | 17.879 | |
| curated_ligrec_stats | 33.238 | 0.761 | 129.534 | |
| database_summary | 1.738 | 0.008 | 3.573 | |
| descendants | 0.013 | 0.000 | 0.013 | |
| ensembl_dataset | 0.013 | 0.000 | 0.013 | |
| ensembl_id_mapping_table | 1.284 | 0.048 | 10.621 | |
| ensembl_id_type | 0.003 | 0.000 | 0.002 | |
| ensembl_name | 0.082 | 0.000 | 0.082 | |
| ensembl_organisms | 0.191 | 0.000 | 0.191 | |
| ensembl_organisms_raw | 0.146 | 0.000 | 0.145 | |
| ensembl_orthology | 0.001 | 0.000 | 0.000 | |
| enzsub_graph | 2.406 | 0.096 | 5.060 | |
| enzsub_resources | 0.082 | 0.004 | 1.021 | |
| enzyme_substrate | 1.191 | 0.008 | 2.137 | |
| evex_download | 0.011 | 0.000 | 0.011 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 14.657 | 0.419 | 17.580 | |
| extra_attrs | 8.260 | 0.119 | 8.401 | |
| extra_attrs_to_cols | 12.950 | 0.108 | 13.092 | |
| filter_by_resource | 7.221 | 0.136 | 8.708 | |
| filter_extra_attrs | 25.706 | 0.176 | 27.998 | |
| filter_intercell | 6.877 | 0.202 | 10.634 | |
| filter_intercell_network | 0.026 | 0.000 | 0.026 | |
| find_all_paths | 6.429 | 0.032 | 6.472 | |
| from_evidences | 0 | 0 | 0 | |
| get_db | 0 | 0 | 0 | |
| get_ontology_db | 0.012 | 0.000 | 0.012 | |
| giant_component | 12.112 | 0.484 | 14.230 | |
| go_annot_download | 13.863 | 0.511 | 27.881 | |
| go_annot_slim | 0 | 0 | 0 | |
| go_ontology_download | 0.008 | 0.004 | 0.028 | |
| guide2pharma_download | 0.012 | 0.000 | 0.029 | |
| harmonizome_download | 0.012 | 0.000 | 0.012 | |
| has_extra_attrs | 7.883 | 0.087 | 8.375 | |
| hmdb_id_mapping_table | 0.012 | 0.000 | 0.023 | |
| hmdb_id_type | 0.003 | 0.000 | 0.003 | |
| hmdb_metabolite_fields | 0.001 | 0.000 | 0.001 | |
| hmdb_protein_fields | 0.000 | 0.000 | 0.001 | |
| hmdb_table | 0.049 | 0.000 | 0.049 | |
| homologene_download | 0.011 | 0.000 | 0.011 | |
| homologene_raw | 0.024 | 0.000 | 0.024 | |
| homologene_uniprot_orthology | 0.011 | 0.000 | 0.011 | |
| hpo_download | 2.437 | 0.226 | 25.027 | |
| htridb_download | 0.012 | 0.000 | 0.013 | |
| id_translation_resources | 0 | 0 | 0 | |
| id_types | 0.098 | 0.000 | 0.099 | |
| inbiomap_download | 0 | 0 | 0 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.371 | 0.012 | 1.105 | |
| interaction_graph | 0.428 | 0.024 | 1.444 | |
| interaction_resources | 0.081 | 0.015 | 1.115 | |
| interaction_types | 0.095 | 0.012 | 0.129 | |
| intercell | 0.478 | 0.028 | 1.720 | |
| intercell_categories | 0.529 | 0.024 | 1.312 | |
| intercell_consensus_filter | 1.524 | 0.023 | 3.839 | |
| intercell_generic_categories | 0.059 | 0.000 | 0.060 | |
| intercell_network | 0.014 | 0.000 | 0.014 | |
| intercell_resources | 0.088 | 0.000 | 1.072 | |
| intercell_summary | 0.060 | 0.000 | 0.117 | |
| is_ontology_id | 0 | 0 | 0 | |
| is_swissprot | 0.037 | 0.000 | 0.082 | |
| is_trembl | 0.079 | 0.000 | 0.154 | |
| is_uniprot | 0.014 | 0.000 | 0.030 | |
| kegg_info | 0.012 | 0.000 | 0.012 | |
| kegg_open | 0.012 | 0.000 | 0.028 | |
| kegg_pathway_annotations | 0 | 0 | 0 | |
| kegg_pathway_download | 0.012 | 0.000 | 0.028 | |
| kegg_pathway_list | 0.005 | 0.007 | 0.028 | |
| kegg_pathways_download | 0 | 0 | 0 | |
| kegg_picture | 0.079 | 0.004 | 1.165 | |
| kegg_process | 0.020 | 0.008 | 0.056 | |
| latin_name | 0.082 | 0.008 | 0.152 | |
| load_db | 0.117 | 0.000 | 0.124 | |
| ncbi_taxid | 0.074 | 0.004 | 0.082 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0.012 | 0.000 | 0.013 | |
| nichenet_gr_network | 0.032 | 0.012 | 0.046 | |
| nichenet_gr_network_evex | 0.014 | 0.000 | 0.013 | |
| nichenet_gr_network_harmonizome | 0.014 | 0.000 | 0.014 | |
| nichenet_gr_network_htridb | 0.013 | 0.000 | 0.013 | |
| nichenet_gr_network_omnipath | 15.630 | 0.344 | 26.874 | |
| nichenet_gr_network_pathwaycommons | 0.012 | 0.000 | 0.013 | |
| nichenet_gr_network_regnetwork | 0.008 | 0.004 | 0.028 | |
| nichenet_gr_network_remap | 0.013 | 0.000 | 0.029 | |
| nichenet_gr_network_trrust | 0.013 | 0.000 | 0.029 | |
| nichenet_ligand_activities | 0 | 0 | 0 | |
| nichenet_ligand_target_links | 0 | 0 | 0 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.078 | 0.000 | 0.157 | |
| nichenet_lr_network_guide2pharma | 0.011 | 0.004 | 0.035 | |
| nichenet_lr_network_omnipath | 0.034 | 0.004 | 0.070 | |
| nichenet_lr_network_ramilowski | 0.009 | 0.004 | 0.029 | |
| nichenet_main | 0 | 0 | 0 | |
| nichenet_networks | 0.066 | 0.000 | 0.130 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.039 | 0.000 | 0.088 | |
| nichenet_results_dir | 0 | 0 | 0 | |
| nichenet_signaling_network | 0.037 | 0.004 | 0.074 | |
| nichenet_signaling_network_cpdb | 0.013 | 0.000 | 0.013 | |
| nichenet_signaling_network_evex | 0.014 | 0.000 | 0.014 | |
| nichenet_signaling_network_harmonizome | 0.014 | 0.000 | 0.014 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 10.493 | 0.071 | 14.170 | |
| nichenet_signaling_network_pathwaycommons | 0.012 | 0.000 | 0.012 | |
| nichenet_signaling_network_vinayagam | 0.011 | 0.000 | 0.011 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.114 | 0.000 | 1.607 | |
| oma_code | 0.041 | 0.000 | 0.089 | |
| oma_organisms | 0.065 | 0.000 | 0.118 | |
| oma_pairwise | 0.012 | 0.000 | 0.012 | |
| oma_pairwise_genesymbols | 0.009 | 0.004 | 0.044 | |
| oma_pairwise_translated | 0.012 | 0.000 | 0.028 | |
| omnipath-interactions | 29.387 | 1.069 | 74.238 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0.009 | 0.000 | 0.009 | |
| omnipath_cache_clean_db | 0.108 | 0.008 | 0.116 | |
| omnipath_cache_download_ready | 0.607 | 0.024 | 0.689 | |
| omnipath_cache_filter_versions | 0.120 | 0.004 | 0.142 | |
| omnipath_cache_get | 0.108 | 0.000 | 0.108 | |
| omnipath_cache_key | 0.001 | 0.000 | 0.001 | |
| omnipath_cache_latest_or_new | 0.076 | 0.000 | 0.077 | |
| omnipath_cache_load | 0.535 | 0.024 | 2.579 | |
| omnipath_cache_move_in | 0.226 | 0.016 | 0.249 | |
| omnipath_cache_remove | 0.115 | 0.004 | 0.124 | |
| omnipath_cache_save | 0.181 | 0.000 | 0.193 | |
| omnipath_cache_search | 0.001 | 0.000 | 0.001 | |
| omnipath_cache_set_ext | 0.094 | 0.000 | 0.099 | |
| omnipath_cache_update_status | 0.141 | 0.000 | 0.141 | |
| omnipath_cache_wipe | 0 | 0 | 0 | |
| omnipath_config_path | 0.001 | 0.000 | 0.001 | |
| omnipath_for_cosmos | 10.246 | 0.191 | 63.700 | |
| omnipath_load_config | 0 | 0 | 0 | |
| omnipath_log | 0 | 0 | 0 | |
| omnipath_logfile | 0.002 | 0.000 | 0.002 | |
| omnipath_msg | 0.007 | 0.000 | 0.007 | |
| omnipath_query | 4.733 | 0.019 | 4.766 | |
| omnipath_reset_config | 0 | 0 | 0 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.03 | 0.00 | 0.03 | |
| omnipath_set_console_loglevel | 0.005 | 0.000 | 0.004 | |
| omnipath_set_logfile_loglevel | 0.005 | 0.000 | 0.004 | |
| omnipath_set_loglevel | 0.003 | 0.000 | 0.002 | |
| omnipath_show_db | 0.071 | 0.000 | 0.071 | |
| omnipath_unlock_cache_db | 0.000 | 0.000 | 0.001 | |
| only_from | 0 | 0 | 0 | |
| ontology_ensure_id | 0.001 | 0.000 | 0.000 | |
| ontology_ensure_name | 0.001 | 0.000 | 0.000 | |
| ontology_name_id | 0.001 | 0.000 | 0.001 | |
| organism_for | 0.053 | 0.000 | 0.053 | |
| pathwaycommons_download | 0 | 0 | 0 | |
| pivot_annotations | 11.173 | 0.313 | 22.058 | |
| preppi_download | 0.001 | 0.000 | 0.001 | |
| preppi_filter | 0.001 | 0.000 | 0.001 | |
| print_bma_motif_es | 0.465 | 0.044 | 1.928 | |
| print_bma_motif_vs | 0.141 | 0.000 | 1.182 | |
| print_interactions | 6.349 | 0.092 | 10.288 | |
| print_path_es | 0.507 | 0.020 | 2.612 | |
| print_path_vs | 2.295 | 0.024 | 5.623 | |
| pubmed_open | 4.675 | 0.008 | 4.689 | |
| query_info | 0.105 | 0.000 | 0.706 | |
| ramilowski_download | 0.001 | 0.000 | 0.001 | |
| ramp_id_mapping_table | 0.001 | 0.000 | 0.001 | |
| ramp_id_type | 0.003 | 0.000 | 0.003 | |
| ramp_sqlite | 0.001 | 0.000 | 0.000 | |
| ramp_table | 0 | 0 | 0 | |
| ramp_tables | 0 | 0 | 0 | |
| regnetwork_directions | 0.000 | 0.000 | 0.001 | |
| regnetwork_download | 0.001 | 0.000 | 0.001 | |
| relations_list_to_table | 0.104 | 0.000 | 0.794 | |
| relations_table_to_graph | 0 | 0 | 0 | |
| relations_table_to_list | 0.087 | 0.004 | 0.374 | |
| remap_dorothea_download | 0 | 0 | 0 | |
| remap_filtered | 0 | 0 | 0 | |
| remap_tf_target_download | 0.000 | 0.000 | 0.001 | |
| resource_info | 0.154 | 0.013 | 1.148 | |
| resources | 0.066 | 0.000 | 1.003 | |
| resources_colname | 0.602 | 0.023 | 2.257 | |
| resources_in | 4.311 | 0.004 | 4.327 | |
| show_network | 0 | 0 | 0 | |
| signed_ptms | 5.569 | 0.004 | 6.620 | |
| simplify_intercell_network | 0.001 | 0.000 | 0.001 | |
| static_table | 6.677 | 0.147 | 11.387 | |
| static_tables | 0.057 | 0.000 | 0.260 | |
| stitch_actions | 0.001 | 0.000 | 0.001 | |
| stitch_links | 0.001 | 0.000 | 0.001 | |
| stitch_network | 0.001 | 0.000 | 0.001 | |
| stitch_remove_prefixes | 0.008 | 0.000 | 0.008 | |
| swap_relations | 0.093 | 0.000 | 0.342 | |
| swissprots_only | 0.041 | 0.000 | 0.040 | |
| tfcensus_download | 0.255 | 0.000 | 0.285 | |
| translate_ids | 1.347 | 0.004 | 20.189 | |
| translate_ids_multi | 8.236 | 0.028 | 17.533 | |
| trembls_only | 0.039 | 0.000 | 0.040 | |
| trrust_download | 0.000 | 0.000 | 0.001 | |
| uniprot_full_id_mapping_table | 0.911 | 0.016 | 96.042 | |
| uniprot_genesymbol_cleanup | 0 | 0 | 0 | |
| uniprot_id_mapping_table | 0.001 | 0.000 | 0.001 | |
| uniprot_id_type | 0.003 | 0.000 | 0.003 | |
| uniprot_idmapping_id_types | 0.183 | 0.016 | 1.485 | |
| unique_intercell_network | 0.001 | 0.000 | 0.001 | |
| unnest_evidences | 0 | 0 | 0 | |
| uploadlists_id_type | 0.002 | 0.000 | 0.002 | |
| vinayagam_download | 0 | 0 | 0 | |
| walk_ontology_tree | 0.001 | 0.000 | 0.001 | |
| with_extra_attrs | 10.994 | 0.127 | 12.633 | |
| with_references | 0.441 | 0.024 | 2.166 | |
| zenodo_download | 0.002 | 0.000 | 0.001 | |